|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PRDM16 |
Gene summary for PRDM16 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRDM16 | Gene ID | 63976 |
| Gene name | PR/SET domain 16 | |
| Gene Alias | CMD1LL | |
| Cytomap | 1p36.32 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q9HAZ2 |
Top |
Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 63976 | PRDM16 | RNA-P17T-P17T-2 | Human | Lung | IAC | 2.53e-04 | 5.65e-01 | 0.3371 |
| 63976 | PRDM16 | RNA-P17T-P17T-4 | Human | Lung | IAC | 1.83e-04 | 6.00e-01 | 0.343 |
| 63976 | PRDM16 | RNA-P17T-P17T-6 | Human | Lung | IAC | 5.18e-03 | 5.18e-01 | 0.3385 |
| 63976 | PRDM16 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 4.01e-05 | 3.44e-01 | -0.2116 |
| 63976 | PRDM16 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 3.10e-02 | 4.09e-01 | -0.1941 |
| 63976 | PRDM16 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 2.91e-02 | 2.32e-01 | -0.2119 |
| 63976 | PRDM16 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 3.40e-02 | 1.84e-01 | -0.0132 |
| 63976 | PRDM16 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 2.67e-04 | 2.10e-01 | -0.013 |
| 63976 | PRDM16 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 4.14e-02 | 1.93e-01 | -0.0121 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
Top |
Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00165704 | Lung | IAC | histone modification | 93/2061 | 463/18723 | 5.41e-09 | 8.03e-07 | 93 |
| GO:00715594 | Lung | IAC | response to transforming growth factor beta | 60/2061 | 256/18723 | 9.50e-09 | 1.25e-06 | 60 |
| GO:00715604 | Lung | IAC | cellular response to transforming growth factor beta stimulus | 57/2061 | 250/18723 | 6.17e-08 | 6.54e-06 | 57 |
| GO:00071794 | Lung | IAC | transforming growth factor beta receptor signaling pathway | 45/2061 | 198/18723 | 1.60e-06 | 7.93e-05 | 45 |
| GO:00063256 | Lung | IAC | chromatin organization | 69/2061 | 409/18723 | 2.01e-04 | 3.53e-03 | 69 |
| GO:00071785 | Lung | IAC | transmembrane receptor protein serine/threonine kinase signaling pathway | 60/2061 | 355/18723 | 4.82e-04 | 7.03e-03 | 60 |
| GO:00454443 | Lung | IAC | fat cell differentiation | 42/2061 | 229/18723 | 6.19e-04 | 8.50e-03 | 42 |
| GO:00349684 | Lung | IAC | histone lysine methylation | 25/2061 | 115/18723 | 6.35e-04 | 8.68e-03 | 25 |
| GO:00182053 | Lung | IAC | peptidyl-lysine modification | 62/2061 | 376/18723 | 7.55e-04 | 9.82e-03 | 62 |
| GO:00180223 | Lung | IAC | peptidyl-lysine methylation | 27/2061 | 131/18723 | 9.41e-04 | 1.14e-02 | 27 |
| GO:19038444 | Lung | IAC | regulation of cellular response to transforming growth factor beta stimulus | 27/2061 | 131/18723 | 9.41e-04 | 1.14e-02 | 27 |
| GO:00064794 | Lung | IAC | protein methylation | 34/2061 | 181/18723 | 1.28e-03 | 1.45e-02 | 34 |
| GO:00082134 | Lung | IAC | protein alkylation | 34/2061 | 181/18723 | 1.28e-03 | 1.45e-02 | 34 |
| GO:00165714 | Lung | IAC | histone methylation | 28/2061 | 141/18723 | 1.39e-03 | 1.53e-02 | 28 |
| GO:00170153 | Lung | IAC | regulation of transforming growth factor beta receptor signaling pathway | 26/2061 | 128/18723 | 1.45e-03 | 1.55e-02 | 26 |
| GO:0030512 | Lung | IAC | negative regulation of transforming growth factor beta receptor signaling pathway | 18/2061 | 81/18723 | 2.68e-03 | 2.46e-02 | 18 |
| GO:0061647 | Lung | IAC | histone H3-K9 modification | 12/2061 | 48/18723 | 4.87e-03 | 3.77e-02 | 12 |
| GO:00515671 | Lung | IAC | histone H3-K9 methylation | 10/2061 | 37/18723 | 5.45e-03 | 4.08e-02 | 10 |
| GO:001657012 | Lung | AIS | histone modification | 81/1849 | 463/18723 | 2.30e-07 | 2.16e-05 | 81 |
| GO:007155912 | Lung | AIS | response to transforming growth factor beta | 51/1849 | 256/18723 | 8.45e-07 | 6.08e-05 | 51 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0471416 | Lung | IAC | Thermogenesis | 46/1053 | 232/8465 | 7.85e-04 | 6.38e-03 | 4.23e-03 | 46 |
| hsa003109 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
| hsa0471417 | Lung | IAC | Thermogenesis | 46/1053 | 232/8465 | 7.85e-04 | 6.38e-03 | 4.23e-03 | 46 |
| hsa0031012 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
| hsa0471423 | Lung | AIS | Thermogenesis | 43/961 | 232/8465 | 7.36e-04 | 6.28e-03 | 4.02e-03 | 43 |
| hsa0031022 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
| hsa0471433 | Lung | AIS | Thermogenesis | 43/961 | 232/8465 | 7.36e-04 | 6.28e-03 | 4.02e-03 | 43 |
| hsa0031032 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
| Page: 1 |
Top |
Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
Top |
Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| PRDM16 | PERI | Colorectum | ADJ | ARL15,NKAIN2,NTRK3, etc. | 5.50e-02 |  |
| PRDM16 | PERI | Colorectum | FAP | ARL15,NKAIN2,NTRK3, etc. | 4.67e-02 |  |
| PRDM16 | PERI | Colorectum | Healthy | ARL15,NKAIN2,NTRK3, etc. | 5.96e-02 |  |
| PRDM16 | MYOFIB | Colorectum | MSS | ARL15,NKAIN2,NTRK3, etc. | 1.72e-01 |  |
| PRDM16 | MSC | Pancreas | ADJ | ZNF708,SORBS2,ARL15, etc. | 3.48e-03 |  |
| PRDM16 | LYMEND | Pancreas | ADJ | ZNF708,SORBS2,ARL15, etc. | 1.97e-01 | |
| PRDM16 | MVA | Skin | cSCC | SEMA3G,MECOM,ARL15, etc. | 1.71e-01 |  |
| PRDM16 | PARI | Stomach | Healthy | ANXA7,RXRA,AP1B1, etc. | 7.45e-02 |  |
| PRDM16 | MVA | Stomach | CSG | PCSK5,IRF7,SEMA3G, etc. | 2.59e-01 |  |
| PRDM16 | MVA | Stomach | GC | PCSK5,IRF7,SEMA3G, etc. | 1.95e-01 |  |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
Top |
Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PRDM16 | SNV | Missense_Mutation | rs768419281 | c.518G>A | p.Arg173His | p.R173H | Q9HAZ2 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-A2-A0EX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PRDM16 | SNV | Missense_Mutation | rs747460948 | c.3487N>A | p.Ala1163Thr | p.A1163T | Q9HAZ2 | protein_coding | tolerated(0.7) | benign(0) | TCGA-A8-A09V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PRDM16 | SNV | Missense_Mutation | c.581A>G | p.Tyr194Cys | p.Y194C | Q9HAZ2 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-B6-A0WZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PRDM16 | SNV | Missense_Mutation | novel | c.1553T>A | p.Phe518Tyr | p.F518Y | Q9HAZ2 | protein_coding | tolerated(0.06) | probably_damaging(0.98) | TCGA-BH-A8FZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PRDM16 | SNV | Missense_Mutation | rs376469401 | c.784N>A | p.Glu262Lys | p.E262K | Q9HAZ2 | protein_coding | tolerated(0.14) | benign(0.003) | TCGA-E9-A22E-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphane | SD |
| PRDM16 | deletion | Frame_Shift_Del | novel | c.2779_2783delNNNNN | p.His927ProfsTer54 | p.H927Pfs*54 | Q9HAZ2 | protein_coding | TCGA-AO-A0JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | leuprolide | SD | ||
| PRDM16 | deletion | Frame_Shift_Del | novel | c.1171delG | p.Val391Ter | p.V391* | Q9HAZ2 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PRDM16 | deletion | Frame_Shift_Del | novel | c.3168delC | p.Ser1057GlnfsTer9 | p.S1057Qfs*9 | Q9HAZ2 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PRDM16 | deletion | Frame_Shift_Del | novel | c.1672delC | p.Leu558TrpfsTer34 | p.L558Wfs*34 | Q9HAZ2 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| PRDM16 | SNV | Missense_Mutation | novel | c.1519T>G | p.Phe507Val | p.F507V | Q9HAZ2 | protein_coding | tolerated(0.07) | benign(0.115) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
Top |
Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |